Abstract
The European Conditional Mouse Mutagenesis (EUCOMM) project aims to establish a mutant resource containing up to 13,000 conditional mouse mutations in C57BL/6N embryonic stem cells. As part of this resource, up to 8,000 targeted conditional mutations will be generated for genes that can not be readily trapped by random gene trapping methods. Non-symmetrical critical exons are identified as part of the targeting approach, which when deleted produce a knockout (KO) transcript that is susceptible to nonsensemediated decay (NMD). The success of this approach is dependent on detailed and accurate genome annotation, which is provided by the Human and Vertebrate Analysis and Annotation (HAVANA) group at the Wellcome Trust Sanger Institute. Based on a combination of EST, cDNA and protein evidence, HAVANA produces high quality manual annotation of gene structures, that includes alternative splice variants, polyadenylation features, pseudogenes and gene family clusters. Using this annotation we are able to identify suitable exons for targeting, whilst minimising potential disruption to adjacent genomic features. Annotation of both gene and KO transcripts can be viewed through the Vertebrate Genome Annotation (VEGA) browser ("http://vega.sanger.ac.uk":http://vega.sanger.ac.uk).More information on the EUCOMM resource and the targeted genes is available at "http://www.eucomm.org":http://www.eucomm.org. Targeting vector design information can also be viewed through the Ensembl genome browser ("http://www.ensembl.org":http://www.ensembl.org) as DAS resources ("http://das.sanger.ac.uk/das/KO_designs":http://das.sanger.ac.uk/das/KO_designs ; "http://das.sanger.ac.uk/das/KO_vectors":http://das.sanger.ac.uk/das/KO_vectors). In addition to the EUCOMM project, HAVANA also contributes towards the mouse Consensus Coding DNA Sequence (CCDS) project and is involved in collaborations with RefSeq and MGI.
Similar content being viewed by others
Article PDF
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Thomas, M. Manual annotation of the mouse genome: HAVANA and EUCOMM. Nat Prec (2009). https://doi.org/10.1038/npre.2009.3181.1
Received:
Accepted:
Published:
DOI: https://doi.org/10.1038/npre.2009.3181.1